› 4v68

Electron Microscopy
6.4Å resolution

T. thermophilus 70S ribosome in complex with mRNA, tRNAs and EF-Tu.GDP.kirromycin ternary complex, fitted to a 6.4 A Cryo-EM map.

Released:
DOI: 10.2210/pdb4v68/pdb
PDB entry 4v68 coloured by chain, front view.
PDB entry 4v68 coloured by chain, side view.
PDB entry 4v68 coloured by chain, top view.
Source organism: Thermus thermophilus
Primary publication:
GTPase activation of elongation factor EF-Tu by the ribosome during decoding.
Schuette JC, Murphy FV, Kelley AC, Weir JR, Giesebrecht J, Connell SR, Loerke J, Mielke T, Zhang W, Penczek PA, Ramakrishnan V, Spahn CM
EMBO J 28 755-65 (2009)
PMID: 19229291
Related structures: EMD-5030

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 60-mer (preferred)
PDBe Complex ID:
PDB-CPX-147922 (preferred)
Entry contents:
52 distinct polypeptide molecules
8 distinct RNA molecules
Macromolecules (60 distinct):
Small ribosomal subunit protein uS2 Chain: AB
Molecule details ›
Chain: AB
Length: 235 amino acids
Theoretical weight: 27.12 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P80371 (Residues: 7-241; Coverage: 92%)
Gene names: TTHA0861, rps2, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS4 Chain: AD
Molecule details ›
Chain: AD
Length: 208 amino acids
Theoretical weight: 24.24 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P80373 (Residues: 2-209; Coverage: 100%)
Gene names: TTHA1665, rps4, rpsD
Sequence domains:
Small ribosomal subunit protein uS5 Chain: AE
Molecule details ›
Chain: AE
Length: 151 amino acids
Theoretical weight: 16.46 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SHQ5 (Residues: 5-155; Coverage: 93%)
Gene names: TTHA1675, rpsE
Sequence domains:
Small ribosomal subunit protein bS6 Chain: AF
Molecule details ›
Chain: AF
Length: 101 amino acids
Theoretical weight: 11.99 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SLP8 (Residues: 1-101; Coverage: 100%)
Gene names: TTHA0245, rpsF
Sequence domains: Ribosomal protein S6
30S ribosomal protein S8 Chain: AH
Molecule details ›
Chain: AH
Length: 138 amino acids
Theoretical weight: 15.87 KDa
Source organism: Thermus thermophilus
Small ribosomal subunit protein uS11 Chain: AK
Molecule details ›
Chain: AK
Length: 119 amino acids
Theoretical weight: 12.61 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P80376 (Residues: 11-129; Coverage: 92%)
Gene names: TTHA1666, rps11, rpsK
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chain: AL
Molecule details ›
Chain: AL
Length: 125 amino acids
Theoretical weight: 13.88 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SHN3 (Residues: 2-126; Coverage: 95%)
Gene names: TTHA1697, rpsL
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS15 Chain: AO
Molecule details ›
Chain: AO
Length: 88 amino acids
Theoretical weight: 10.45 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SJ76 (Residues: 2-89; Coverage: 99%)
Gene names: TTHA1138, rpsO
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16 Chain: AP
Molecule details ›
Chain: AP
Length: 84 amino acids
Theoretical weight: 10 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SJH3 (Residues: 1-84; Coverage: 96%)
Gene names: TTHA1035, rpsP
Sequence domains: Ribosomal protein S16
30S ribosomal protein S17 Chain: AQ
Molecule details ›
Chain: AQ
Length: 100 amino acids
Theoretical weight: 11.88 KDa
Source organism: Thermus thermophilus
Small ribosomal subunit protein bS18 Chain: AR
Molecule details ›
Chain: AR
Length: 70 amino acids
Theoretical weight: 8.16 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SLQ0 (Residues: 19-88; Coverage: 80%)
Gene names: TTHA0243, rpsR
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein bS20 Chain: AT
Molecule details ›
Chain: AT
Length: 99 amino acids
Theoretical weight: 10.92 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P80380 (Residues: 8-106; Coverage: 93%)
Gene names: TTHA1397, rps20, rpsT
Sequence domains: Ribosomal protein S20
Small ribosomal subunit protein uS3 Chain: AC
Molecule details ›
Chain: AC
Length: 207 amino acids
Theoretical weight: 22.98 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P80372 (Residues: 2-208; Coverage: 87%)
Gene names: TTHA1686, rps3, rpsC
Sequence domains:
Small ribosomal subunit protein uS7 Chain: AG
Molecule details ›
Chain: AG
Length: 155 amino acids
Theoretical weight: 17.92 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P17291 (Residues: 2-156; Coverage: 99%)
Gene names: TTHA1696, rps7, rpsG
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS9 Chain: AI
Molecule details ›
Chain: AI
Length: 127 amino acids
Theoretical weight: 14.3 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P62669 (Residues: 2-128; Coverage: 99%)
Gene names: TT_C1100, rps9, rpsI
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10 Chain: AJ
Molecule details ›
Chain: AJ
Length: 99 amino acids
Theoretical weight: 11.4 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SHN7 (Residues: 3-101; Coverage: 94%)
Gene names: TTHA1693, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS13 Chain: AM
Molecule details ›
Chain: AM
Length: 125 amino acids
Theoretical weight: 14.21 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P80377 (Residues: 2-126; Coverage: 99%)
Gene names: TTHA1667, rps13, rpsM
Sequence domains: Ribosomal protein S13/S18
30S ribosomal protein S14 Chain: AN
Molecule details ›
Chain: AN
Length: 60 amino acids
Theoretical weight: 7.03 KDa
Source organism: Thermus thermophilus
Small ribosomal subunit protein uS19 Chain: AS
Molecule details ›
Chain: AS
Length: 79 amino acids
Theoretical weight: 9.01 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SHP2 (Residues: 4-82; Coverage: 85%)
Gene names: TTHA1688, rpsS
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein bTHX Chain: AU
Molecule details ›
Chain: AU
Length: 25 amino acids
Theoretical weight: 3.09 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SIH3 (Residues: 2-26; Coverage: 93%)
Gene names: TTHA1396, rpsU
Sequence domains: 30S ribosomal protein Thx
Elongation factor Tu-B Chain: AZ
Molecule details ›
Chain: AZ
Length: 405 amino acids
Theoretical weight: 44.71 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P60339 (Residues: 2-406; Coverage: 100%)
Gene names: TTHA0251, tufB
Sequence domains:
Large ribosomal subunit protein bL27 Chain: B0
Molecule details ›
Chain: B0
Length: 85 amino acids
Theoretical weight: 9.53 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P60493 (Residues: 1-85; Coverage: 100%)
Gene names: TTHA1782, rpmA
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein bL28 Chain: B1
Molecule details ›
Chain: B1
Length: 89 amino acids
Theoretical weight: 9.99 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P60494 (Residues: 8-96; Coverage: 91%)
Gene names: TTHA0042, rpmB
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein uL29 Chain: B2
Molecule details ›
Chain: B2
Length: 51 amino acids
Theoretical weight: 6.11 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SHP6 (Residues: 12-62; Coverage: 71%)
Gene names: TTHA1684, rpmC
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL30 Chain: B3
Molecule details ›
Chain: B3
Length: 60 amino acids
Theoretical weight: 6.8 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SHQ6 (Residues: 1-60; Coverage: 100%)
Gene names: TTHA1674, rpmD
Sequence domains: Ribosomal protein L30p/L7e
Large ribosomal subunit protein bL31 Chain: B4
Molecule details ›
Chain: B4
Length: 50 amino acids
Theoretical weight: 5.68 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SJE1 (Residues: 1-50; Coverage: 70%)
Gene names: TTHA1073, rpmE
Sequence domains: Ribosomal protein L31
Large ribosomal subunit protein bL32 Chain: B5
Molecule details ›
Chain: B5
Length: 59 amino acids
Theoretical weight: 6.59 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P80339 (Residues: 2-60; Coverage: 98%)
Gene names: TTHA0418, rpl32, rpmF
Sequence domains: Ribosomal L32p protein family
Large ribosomal subunit protein bL33 Chain: B6
Molecule details ›
Chain: B6
Length: 45 amino acids
Theoretical weight: 5.6 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P35871 (Residues: 9-53; Coverage: 83%)
Gene names: TTHA0250, rpl33, rpmG
Sequence domains: Ribosomal protein L33
Large ribosomal subunit protein bL34 Chain: B7
Molecule details ›
Chain: B7
Length: 49 amino acids
Theoretical weight: 6.13 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P80340 (Residues: 1-49; Coverage: 100%)
Gene names: TTHA0446, rpl34, rpmH
Sequence domains: Ribosomal protein L34
Large ribosomal subunit protein bL35 Chain: B8
Molecule details ›
Chain: B8
Length: 64 amino acids
Theoretical weight: 7.37 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P80341 (Residues: 2-65; Coverage: 99%)
Gene names: rpl35, rpmI
Sequence domains: Ribosomal protein L35
Large ribosomal subunit protein bL36 Chain: B9
Molecule details ›
Chain: B9
Length: 35 amino acids
Theoretical weight: 4.25 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q72I28 (Residues: 2-36; Coverage: 95%)
Gene names: TT_C1304, rpmJ
Sequence domains: Ribosomal protein L36
Large ribosomal subunit protein uL1 Chain: BC
Molecule details ›
Chain: BC
Length: 191 amino acids
Theoretical weight: 20.66 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SLP7 (Residues: 19-225; Coverage: 83%)
Gene names: TTHA0246, rplA
Sequence domains: Ribosomal protein L1p/L10e family
Large ribosomal subunit protein uL2 Chain: BD
Molecule details ›
Chain: BD
Length: 272 amino acids
Theoretical weight: 29.99 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P60405 (Residues: 2-273; Coverage: 99%)
Gene names: TTHA1689, rplB
Sequence domains:
Large ribosomal subunit protein uL3 Chain: BE
Molecule details ›
Chain: BE
Length: 205 amino acids
Theoretical weight: 22.32 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SHN8 (Residues: 1-205; Coverage: 100%)
Gene names: TTHA1692, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chain: BF
Molecule details ›
Chain: BF
Length: 208 amino acids
Theoretical weight: 23.07 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SHN9 (Residues: 1-208; Coverage: 99%)
Gene names: TTHA1691, rplD
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5 Chain: BG
Molecule details ›
Chain: BG
Length: 181 amino acids
Theoretical weight: 20.93 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SHQ0 (Residues: 2-182; Coverage: 100%)
Gene names: TTHA1680, rplE
Sequence domains:
50S ribosomal protein L6 Chain: BH
Molecule details ›
Chain: BH
Length: 160 amino acids
Theoretical weight: 17.48 KDa
Source organism: Thermus thermophilus
Large ribosomal subunit protein bL9 Chain: BI
Molecule details ›
Chain: BI
Length: 146 amino acids
Theoretical weight: 16.19 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SLQ1 (Residues: 1-146; Coverage: 99%)
Gene names: TTHA0242, rplI
Sequence domains:
Large ribosomal subunit protein uL11 Chain: BL
Molecule details ›
Chain: BL
Length: 138 amino acids
Theoretical weight: 14.63 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P36238 (Residues: 2-139; Coverage: 94%)
Gene names: rpl11, rplK
Sequence domains:
Large ribosomal subunit protein uL13 Chain: BN
Molecule details ›
Chain: BN
Length: 139 amino acids
Theoretical weight: 15.83 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P60488 (Residues: 1-139; Coverage: 99%)
Gene names: TTHA1465, rplM
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14 Chain: BO
Molecule details ›
Chain: BO
Length: 122 amino acids
Theoretical weight: 13.32 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SHP8 (Residues: 1-122; Coverage: 100%)
Gene names: TTHA1682, rplN
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL15 Chain: BP
Molecule details ›
Chain: BP
Length: 146 amino acids
Theoretical weight: 15.86 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SHQ7 (Residues: 5-150; Coverage: 97%)
Gene names: TTHA1673, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL16 Chain: BQ
Molecule details ›
Chain: BQ
Length: 136 amino acids
Theoretical weight: 15.36 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P60489 (Residues: 6-141; Coverage: 97%)
Gene names: TTHA1685, rplP
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein bL17 Chain: BR
Molecule details ›
Chain: BR
Length: 117 amino acids
Theoretical weight: 13.62 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q9Z9H5 (Residues: 2-118; Coverage: 99%)
Gene names: TTHA1663, rpl17, rplQ
Sequence domains: Ribosomal protein L17
Large ribosomal subunit protein uL18 Chain: BS
Molecule details ›
Chain: BS
Length: 99 amino acids
Theoretical weight: 11 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SHQ4 (Residues: 11-109; Coverage: 88%)
Gene names: TTHA1676, rplR
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Large ribosomal subunit protein bL19 Chain: BT
Molecule details ›
Chain: BT
Length: 138 amino acids
Theoretical weight: 16.29 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P60490 (Residues: 1-138; Coverage: 95%)
Gene names: TTHA1031, rplS
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL20 Chain: BU
Molecule details ›
Chain: BU
Length: 117 amino acids
Theoretical weight: 13.65 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P60491 (Residues: 2-118; Coverage: 99%)
Gene names: TTHA0553, rplT
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21 Chain: BV
Molecule details ›
Chain: BV
Length: 101 amino acids
Theoretical weight: 11.07 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P60492 (Residues: 1-101; Coverage: 100%)
Gene names: TTHA1783, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22 Chain: BW
Molecule details ›
Chain: BW
Length: 113 amino acids
Theoretical weight: 12.81 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SHP3 (Residues: 1-113; Coverage: 100%)
Gene names: TTHA1687, rplV
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL23 Chain: BX
Molecule details ›
Chain: BX
Length: 93 amino acids
Theoretical weight: 10.39 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SHP0 (Residues: 3-95; Coverage: 97%)
Gene names: TTHA1690, rplW
Sequence domains: Ribosomal protein L23
Large ribosomal subunit protein uL24 Chain: BY
Molecule details ›
Chain: BY
Length: 101 amino acids
Theoretical weight: 11.18 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SHP9 (Residues: 2-102; Coverage: 92%)
Gene names: TTHA1681, rplX
Sequence domains:
Large ribosomal subunit protein bL25 Chain: BZ
Molecule details ›
Chain: BZ
Length: 177 amino acids
Theoretical weight: 20.01 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SHZ1 (Residues: 3-179; Coverage: 86%)
Gene names: TTHA1589, rpl25, rplY, rptL5
Sequence domains:
16S ribosomal RNA Chain: AA
Molecule details ›
Chain: AA
Length: 1504 nucleotides
Theoretical weight: 488.39 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
P-SITE TRNA Chain: AV
Molecule details ›
Chain: AV
Length: 77 nucleotides
Theoretical weight: 24.82 KDa
Sequence domains: tRNA
SYNTHETIC MRNA Chain: AX
Molecule details ›
Chain: AX
Length: 6 nucleotides
Theoretical weight: 1.92 KDa
E-SITE TRNA Chain: AW
Molecule details ›
Chain: AW
Length: 76 nucleotides
Theoretical weight: 24.49 KDa
Sequence domains: tRNA
AT-SITE TRNA Chain: AY
Molecule details ›
Chain: AY
Length: 72 nucleotides
Theoretical weight: 23.58 KDa
Sequence domains: tRNA
MRNA CODON Chain: A0
Molecule details ›
Chain: A0
Length: 3 nucleotides
Theoretical weight: 874 Da
23S ribosomal RNA Chain: BA
Molecule details ›
Chain: BA
Length: 2852 nucleotides
Theoretical weight: 927.66 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: BB
Molecule details ›
Chain: BB
Length: 119 nucleotides
Theoretical weight: 38.55 KDa
Sequence domains: 5S ribosomal RNA

Ligands and Environments

4 bound ligands:
Ligand PHA 1 x PHA
Ligand GDP 1 x GDP
Ligand MAU 1 x MAU
Ligand BME 1 x BME
10 modified residues:
Ligand 5MU 2 x 5MU
Ligand 2MG 1 x 2MG
Ligand M2G 1 x M2G
Ligand OMC 1 x OMC
Ligand OMG 1 x OMG
Ligand YG 1 x YG
Ligand PSU 2 x PSU
Ligand 5MC 2 x 5MC
Ligand 7MG 1 x 7MG
Ligand 1MA 1 x 1MA

Experiments and Validation Details

Entry percentile scores
Resolution: 6.4Å
Relevant EMDB volumes: EMD-5030

Quick links

Citations

32 review citations

What recent ribosome structures have revealed about the mechanism of translation.
Schmeing et al. (2009)
31 more

4 mentions without citation

Endogenous rRNA Sequence Variation Can Regulate Stress Response Gene Expression and Phenotype.
Kurylo et al. (2018)
3 more